Added custom validation to PydSubmission to replace 'finalize_parse'

src/submissions/backend/db/models/submissions.py

@@ -817,7 +817,7 @@ class BasicSubmission(BaseClass):
         return input_dict
 
     @classmethod
-    def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None) -> dict:
+    def custom_validation(cls, pyd:"PydSubmission") -> dict:
         """
         Performs any final custom parsing of the excel file.
 
@@ -831,7 +831,7 @@ class BasicSubmission(BaseClass):
             dict: Updated parser product.
         """
         logger.info(f"Called {cls.__mapper_args__['polymorphic_identity']} finalizer")
-        return input_dict
+        return pyd
 
     @classmethod
     def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False,
@@ -1390,7 +1390,7 @@ class BacterialCulture(BasicSubmission):
         return template
 
     @classmethod
-    def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None) -> dict:
+    def custom_validation(cls, pyd) -> dict:
         """
         Extends parent. Currently finds control sample and adds to reagents.
 
@@ -1403,24 +1403,24 @@ class BacterialCulture(BasicSubmission):
             dict: Updated dictionary.
         """
         from . import ControlType
-        input_dict = super().finalize_parse(input_dict, xl, info_map)
+        pyd = super().custom_validation(pyd)
         # NOTE: build regex for all control types that have targets
         regex = ControlType.build_positive_regex()
         # NOTE: search samples for match
-        for sample in input_dict['samples']:
-            matched = regex.match(sample['submitter_id'])
+        for sample in pyd.samples:
+            matched = regex.match(sample.submitter_id)
             if bool(matched):
                 # logger.debug(f"Control match found: {sample['submitter_id']}")
                 new_lot = matched.group()
                 try:
                     pos_control_reg = \
-                        next(reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control")
+                        next(reg for reg in pyd.reagents if reg.role == "Bacterial-Positive Control")
                 except StopIteration:
                     logger.error(f"No positive control reagent listed")
-                    return input_dict
-                pos_control_reg['lot'] = new_lot
-                pos_control_reg['missing'] = False
-        return input_dict
+                    return pyd
+                pos_control_reg.lot = new_lot
+                pos_control_reg.missing = False
+        return pyd
 
     # @classmethod
     # def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
@@ -1812,6 +1812,21 @@ class WastewaterArtic(BasicSubmission):
                 continue
             else:
                 datum['plate'] = RSLNamer(filename=datum['plate'], sub_type="Wastewater").parsed_name
+        if xl is not None:
+            try:
+                input_dict['csv'] = xl["hitpicks_csv_to_export"]
+            except KeyError as e:
+                logger.error(e)
+                try:
+                    match input_dict['rsl_plate_num']:
+                        case dict():
+                            input_dict['csv'] = xl[input_dict['rsl_plate_num']['value']]
+                        case str():
+                            input_dict['csv'] = xl[input_dict['rsl_plate_num']]
+                        case _:
+                            pass
+                except Exception as e:
+                    logger.error(f"Error handling couldn't get csv due to: {e}")
         input_dict['source_plates'] = data
         egel_info_section = custom_fields['egel_info']
         ws = xl[egel_info_section['sheet']]
@@ -1992,7 +2007,7 @@ class WastewaterArtic(BasicSubmission):
         return final_en_name
 
     @classmethod
-    def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None) -> dict:
+    def custom_validation(cls, pyd) -> dict:
         """
         Performs any final custom parsing of the excel file. Extends parent
 
@@ -2005,13 +2020,13 @@ class WastewaterArtic(BasicSubmission):
         Returns:
             dict: Updated parser product.
         """
-        input_dict = super().finalize_parse(input_dict, xl, info_map)
+        input_dict = super().custom_validation(pyd)
         # logger.debug(f"Incoming input_dict: {pformat(input_dict)}")
-        for sample in input_dict['samples']:
+        for sample in pyd.samples:
             # logger.debug(f"Sample: {sample}")
-            if re.search(r"^NTC", sample['submitter_id']):
-                sample['submitter_id'] = f"{sample['submitter_id']}-WWG-{input_dict['rsl_plate_num']['value']}"
-        input_dict['csv'] = xl["hitpicks_csv_to_export"]
+            if re.search(r"^NTC", sample.submitter_id):
+                sample.submitter_id = f"{sample.submitter_id}-WWG-{pyd.rsl_plate_num}"
+        # input_dict['csv'] = xl["hitpicks_csv_to_export"]
         return input_dict
 
     @classmethod